Multiple sequence alignment - TraesCS3B01G030300
BLAST Results
Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.
qseqid | sseqid | percentage.identical | alignment.length | no.mismatch | no.gap.openings | qstart | qend | sstart | send | evalue | bitscore | |
---|---|---|---|---|---|---|---|---|---|---|---|---|
0 | TraesCS3B01G030300 | chr3B | 100.000 | 2872 | 0 | 0 | 479 | 3350 | 13906179 | 13903308 | 0.000000e+00 | 5304.0 |
1 | TraesCS3B01G030300 | chr3B | 80.328 | 488 | 55 | 17 | 479 | 947 | 259244110 | 259243645 | 6.930000e-87 | 331.0 |
2 | TraesCS3B01G030300 | chr3B | 100.000 | 148 | 0 | 0 | 1 | 148 | 13906657 | 13906510 | 1.180000e-69 | 274.0 |
3 | TraesCS3B01G030300 | chr3B | 88.073 | 218 | 26 | 0 | 3094 | 3311 | 225255844 | 225256061 | 3.320000e-65 | 259.0 |
4 | TraesCS3B01G030300 | chr3B | 94.444 | 144 | 8 | 0 | 4 | 147 | 259244272 | 259244129 | 4.350000e-54 | 222.0 |
5 | TraesCS3B01G030300 | chr3B | 90.588 | 170 | 12 | 1 | 703 | 868 | 259244310 | 259244479 | 4.350000e-54 | 222.0 |
6 | TraesCS3B01G030300 | chr3B | 86.339 | 183 | 19 | 3 | 688 | 870 | 13906648 | 13906824 | 9.480000e-46 | 195.0 |
7 | TraesCS3B01G030300 | chr3A | 87.593 | 669 | 55 | 6 | 2710 | 3350 | 715554781 | 715554113 | 0.000000e+00 | 750.0 |
8 | TraesCS3B01G030300 | chr3A | 87.225 | 227 | 29 | 0 | 3094 | 3320 | 738332843 | 738332617 | 3.320000e-65 | 259.0 |
9 | TraesCS3B01G030300 | chr5A | 87.126 | 668 | 58 | 6 | 2711 | 3350 | 8500752 | 8500085 | 0.000000e+00 | 732.0 |
10 | TraesCS3B01G030300 | chr4A | 82.665 | 623 | 80 | 18 | 2711 | 3314 | 201632816 | 201632203 | 8.230000e-146 | 527.0 |
11 | TraesCS3B01G030300 | chr4A | 84.483 | 406 | 41 | 13 | 2711 | 3097 | 536785524 | 536785122 | 6.780000e-102 | 381.0 |
12 | TraesCS3B01G030300 | chr4A | 78.808 | 453 | 70 | 19 | 2230 | 2667 | 681609357 | 681609798 | 7.080000e-72 | 281.0 |
13 | TraesCS3B01G030300 | chr5B | 82.287 | 621 | 81 | 17 | 2714 | 3314 | 34783280 | 34782669 | 8.290000e-141 | 510.0 |
14 | TraesCS3B01G030300 | chr5B | 84.892 | 278 | 31 | 9 | 523 | 793 | 248753706 | 248753979 | 1.530000e-68 | 270.0 |
15 | TraesCS3B01G030300 | chr5B | 83.849 | 291 | 20 | 12 | 689 | 953 | 248753539 | 248753250 | 5.550000e-63 | 252.0 |
16 | TraesCS3B01G030300 | chr5B | 84.556 | 259 | 30 | 6 | 705 | 953 | 248753920 | 248754178 | 7.180000e-62 | 248.0 |
17 | TraesCS3B01G030300 | chr5B | 93.007 | 143 | 10 | 0 | 1 | 143 | 248753531 | 248753673 | 3.390000e-50 | 209.0 |
18 | TraesCS3B01G030300 | chr5B | 87.681 | 138 | 11 | 2 | 816 | 947 | 679821262 | 679821125 | 4.480000e-34 | 156.0 |
19 | TraesCS3B01G030300 | chr5B | 84.932 | 146 | 17 | 4 | 812 | 952 | 68422887 | 68422742 | 3.480000e-30 | 143.0 |
20 | TraesCS3B01G030300 | chr4D | 81.947 | 637 | 79 | 24 | 2710 | 3316 | 43264329 | 43263699 | 1.070000e-139 | 507.0 |
21 | TraesCS3B01G030300 | chr4D | 80.938 | 341 | 36 | 14 | 2710 | 3033 | 477534482 | 477534154 | 3.340000e-60 | 243.0 |
22 | TraesCS3B01G030300 | chrUn | 94.521 | 292 | 16 | 0 | 957 | 1248 | 32344440 | 32344731 | 5.100000e-123 | 451.0 |
23 | TraesCS3B01G030300 | chrUn | 96.907 | 97 | 3 | 0 | 2130 | 2226 | 32344727 | 32344823 | 2.670000e-36 | 163.0 |
24 | TraesCS3B01G030300 | chr2B | 91.746 | 315 | 24 | 2 | 479 | 793 | 601205763 | 601206075 | 1.430000e-118 | 436.0 |
25 | TraesCS3B01G030300 | chr2B | 92.213 | 244 | 13 | 3 | 2414 | 2651 | 29705987 | 29706230 | 1.150000e-89 | 340.0 |
26 | TraesCS3B01G030300 | chr2B | 85.886 | 333 | 28 | 6 | 479 | 793 | 334699625 | 334699956 | 1.490000e-88 | 337.0 |
27 | TraesCS3B01G030300 | chr2B | 86.364 | 308 | 23 | 2 | 479 | 786 | 694048110 | 694048398 | 5.390000e-83 | 318.0 |
28 | TraesCS3B01G030300 | chr2B | 72.361 | 1165 | 251 | 52 | 1106 | 2222 | 17503174 | 17502033 | 5.430000e-78 | 302.0 |
29 | TraesCS3B01G030300 | chr2B | 72.208 | 1137 | 228 | 48 | 1142 | 2222 | 17515160 | 17514056 | 5.510000e-68 | 268.0 |
30 | TraesCS3B01G030300 | chr2B | 89.524 | 210 | 16 | 4 | 2453 | 2658 | 691266679 | 691266472 | 9.220000e-66 | 261.0 |
31 | TraesCS3B01G030300 | chr2B | 80.060 | 331 | 48 | 14 | 523 | 842 | 217801328 | 217801005 | 2.600000e-56 | 230.0 |
32 | TraesCS3B01G030300 | chr2B | 71.707 | 1078 | 216 | 55 | 1197 | 2218 | 17444261 | 17445305 | 5.630000e-53 | 219.0 |
33 | TraesCS3B01G030300 | chr2B | 93.750 | 144 | 9 | 0 | 1 | 144 | 601205601 | 601205744 | 2.020000e-52 | 217.0 |
34 | TraesCS3B01G030300 | chr2B | 93.662 | 142 | 9 | 0 | 1 | 142 | 334699461 | 334699602 | 2.620000e-51 | 213.0 |
35 | TraesCS3B01G030300 | chr2B | 81.315 | 289 | 31 | 11 | 689 | 958 | 601205609 | 601205325 | 2.620000e-51 | 213.0 |
36 | TraesCS3B01G030300 | chr2B | 94.161 | 137 | 8 | 0 | 11 | 147 | 39881080 | 39880944 | 3.390000e-50 | 209.0 |
37 | TraesCS3B01G030300 | chr2B | 92.414 | 145 | 11 | 0 | 1 | 145 | 694047946 | 694048090 | 1.220000e-49 | 207.0 |
38 | TraesCS3B01G030300 | chr2B | 92.908 | 141 | 10 | 0 | 5 | 145 | 453795701 | 453795841 | 4.380000e-49 | 206.0 |
39 | TraesCS3B01G030300 | chr2B | 79.336 | 271 | 44 | 11 | 1144 | 1411 | 17144072 | 17144333 | 2.660000e-41 | 180.0 |
40 | TraesCS3B01G030300 | chr2B | 85.294 | 136 | 12 | 3 | 1278 | 1411 | 5782141 | 5782012 | 2.100000e-27 | 134.0 |
41 | TraesCS3B01G030300 | chr1B | 87.705 | 366 | 37 | 6 | 481 | 842 | 567761980 | 567762341 | 1.440000e-113 | 420.0 |
42 | TraesCS3B01G030300 | chr1B | 90.614 | 277 | 25 | 1 | 504 | 779 | 587809215 | 587808939 | 1.900000e-97 | 366.0 |
43 | TraesCS3B01G030300 | chr1B | 84.556 | 259 | 30 | 5 | 705 | 953 | 567762261 | 567762519 | 7.180000e-62 | 248.0 |
44 | TraesCS3B01G030300 | chr1B | 83.137 | 255 | 28 | 7 | 703 | 952 | 587809402 | 587809646 | 5.630000e-53 | 219.0 |
45 | TraesCS3B01G030300 | chr6D | 85.230 | 413 | 36 | 16 | 2256 | 2657 | 454211326 | 454210928 | 5.210000e-108 | 401.0 |
46 | TraesCS3B01G030300 | chr6D | 83.538 | 407 | 46 | 12 | 2709 | 3097 | 216863194 | 216862791 | 8.840000e-96 | 361.0 |
47 | TraesCS3B01G030300 | chr6D | 85.401 | 137 | 18 | 2 | 479 | 615 | 47676996 | 47677130 | 1.250000e-29 | 141.0 |
48 | TraesCS3B01G030300 | chr7D | 83.784 | 407 | 45 | 12 | 2709 | 3097 | 475721650 | 475721247 | 1.900000e-97 | 366.0 |
49 | TraesCS3B01G030300 | chr7D | 72.561 | 1148 | 242 | 35 | 1122 | 2222 | 21773849 | 21774970 | 1.170000e-79 | 307.0 |
50 | TraesCS3B01G030300 | chr7D | 82.353 | 340 | 41 | 12 | 2711 | 3033 | 582519853 | 582519516 | 9.150000e-71 | 278.0 |
51 | TraesCS3B01G030300 | chr1D | 92.742 | 248 | 14 | 3 | 2414 | 2657 | 486401898 | 486401651 | 4.110000e-94 | 355.0 |
52 | TraesCS3B01G030300 | chr2A | 73.054 | 1169 | 236 | 51 | 1106 | 2222 | 11983249 | 11982108 | 1.150000e-89 | 340.0 |
53 | TraesCS3B01G030300 | chr6B | 90.800 | 250 | 16 | 5 | 2414 | 2657 | 47929207 | 47929455 | 8.960000e-86 | 327.0 |
54 | TraesCS3B01G030300 | chr6B | 86.014 | 286 | 20 | 7 | 2709 | 2974 | 134815005 | 134815290 | 4.230000e-74 | 289.0 |
55 | TraesCS3B01G030300 | chr6B | 88.073 | 218 | 26 | 0 | 3094 | 3311 | 18451904 | 18452121 | 3.320000e-65 | 259.0 |
56 | TraesCS3B01G030300 | chr6B | 93.662 | 142 | 9 | 0 | 4 | 145 | 687410826 | 687410685 | 2.620000e-51 | 213.0 |
57 | TraesCS3B01G030300 | chr6B | 88.194 | 144 | 16 | 1 | 490 | 633 | 153675289 | 153675431 | 1.600000e-38 | 171.0 |
58 | TraesCS3B01G030300 | chr5D | 90.361 | 249 | 20 | 3 | 2414 | 2658 | 79640498 | 79640250 | 1.160000e-84 | 324.0 |
59 | TraesCS3B01G030300 | chr5D | 82.111 | 341 | 42 | 12 | 2710 | 3033 | 298522233 | 298521895 | 1.180000e-69 | 274.0 |
60 | TraesCS3B01G030300 | chr5D | 78.088 | 502 | 53 | 24 | 479 | 952 | 545817341 | 545817813 | 7.130000e-67 | 265.0 |
61 | TraesCS3B01G030300 | chr2D | 92.718 | 206 | 11 | 3 | 2456 | 2657 | 609295474 | 609295679 | 9.090000e-76 | 294.0 |
62 | TraesCS3B01G030300 | chr7B | 87.225 | 227 | 29 | 0 | 3094 | 3320 | 99795708 | 99795482 | 3.320000e-65 | 259.0 |
63 | TraesCS3B01G030300 | chr7B | 87.225 | 227 | 29 | 0 | 3094 | 3320 | 125247760 | 125247534 | 3.320000e-65 | 259.0 |
64 | TraesCS3B01G030300 | chr7B | 87.225 | 227 | 29 | 0 | 3094 | 3320 | 125283815 | 125283589 | 3.320000e-65 | 259.0 |
65 | TraesCS3B01G030300 | chr7B | 88.073 | 218 | 26 | 0 | 3094 | 3311 | 628353730 | 628353947 | 3.320000e-65 | 259.0 |
66 | TraesCS3B01G030300 | chr7B | 86.784 | 227 | 30 | 0 | 3094 | 3320 | 125317696 | 125317470 | 1.540000e-63 | 254.0 |
67 | TraesCS3B01G030300 | chr7B | 76.600 | 500 | 81 | 26 | 479 | 952 | 73897116 | 73897605 | 3.340000e-60 | 243.0 |
68 | TraesCS3B01G030300 | chr7B | 82.917 | 240 | 37 | 3 | 2422 | 2657 | 22716499 | 22716260 | 2.620000e-51 | 213.0 |
69 | TraesCS3B01G030300 | chr7B | 79.832 | 119 | 20 | 4 | 2242 | 2357 | 700894371 | 700894254 | 2.140000e-12 | 84.2 |
70 | TraesCS3B01G030300 | chr4B | 87.500 | 224 | 27 | 1 | 3094 | 3316 | 30592902 | 30593125 | 1.190000e-64 | 257.0 |
71 | TraesCS3B01G030300 | chr7A | 92.571 | 175 | 9 | 3 | 2487 | 2657 | 1475882 | 1475708 | 7.180000e-62 | 248.0 |
72 | TraesCS3B01G030300 | chr7A | 71.603 | 1148 | 253 | 40 | 1122 | 2222 | 22198099 | 22199220 | 2.580000e-61 | 246.0 |
73 | TraesCS3B01G030300 | chr7A | 86.164 | 159 | 16 | 6 | 2234 | 2389 | 1476126 | 1475971 | 2.070000e-37 | 167.0 |
74 | TraesCS3B01G030300 | chr7A | 84.906 | 159 | 19 | 5 | 2234 | 2389 | 1476539 | 1476383 | 4.480000e-34 | 156.0 |
75 | TraesCS3B01G030300 | chr7A | 86.301 | 146 | 14 | 3 | 812 | 953 | 105425657 | 105425800 | 1.610000e-33 | 154.0 |
76 | TraesCS3B01G030300 | chr3D | 95.556 | 135 | 6 | 0 | 11 | 145 | 300711890 | 300711756 | 2.020000e-52 | 217.0 |
These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.
query | scaffold | start | end | length | rev.comp | avg.bitscore | max.bitscore | avg.percent.identical | query.start | query.end | num_hsp | groupid | homo_length | |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
0 | TraesCS3B01G030300 | chr3B | 13903308 | 13906657 | 3349 | True | 2789.000000 | 5304 | 100.0000 | 1 | 3350 | 2 | chr3B.!!$R1 | 3349 |
1 | TraesCS3B01G030300 | chr3B | 259243645 | 259244272 | 627 | True | 276.500000 | 331 | 87.3860 | 4 | 947 | 2 | chr3B.!!$R2 | 943 |
2 | TraesCS3B01G030300 | chr3A | 715554113 | 715554781 | 668 | True | 750.000000 | 750 | 87.5930 | 2710 | 3350 | 1 | chr3A.!!$R1 | 640 |
3 | TraesCS3B01G030300 | chr5A | 8500085 | 8500752 | 667 | True | 732.000000 | 732 | 87.1260 | 2711 | 3350 | 1 | chr5A.!!$R1 | 639 |
4 | TraesCS3B01G030300 | chr4A | 201632203 | 201632816 | 613 | True | 527.000000 | 527 | 82.6650 | 2711 | 3314 | 1 | chr4A.!!$R1 | 603 |
5 | TraesCS3B01G030300 | chr5B | 34782669 | 34783280 | 611 | True | 510.000000 | 510 | 82.2870 | 2714 | 3314 | 1 | chr5B.!!$R1 | 600 |
6 | TraesCS3B01G030300 | chr5B | 248753531 | 248754178 | 647 | False | 242.333333 | 270 | 87.4850 | 1 | 953 | 3 | chr5B.!!$F1 | 952 |
7 | TraesCS3B01G030300 | chr4D | 43263699 | 43264329 | 630 | True | 507.000000 | 507 | 81.9470 | 2710 | 3316 | 1 | chr4D.!!$R1 | 606 |
8 | TraesCS3B01G030300 | chr2B | 17502033 | 17503174 | 1141 | True | 302.000000 | 302 | 72.3610 | 1106 | 2222 | 1 | chr2B.!!$R2 | 1116 |
9 | TraesCS3B01G030300 | chr2B | 17514056 | 17515160 | 1104 | True | 268.000000 | 268 | 72.2080 | 1142 | 2222 | 1 | chr2B.!!$R3 | 1080 |
10 | TraesCS3B01G030300 | chr2B | 17444261 | 17445305 | 1044 | False | 219.000000 | 219 | 71.7070 | 1197 | 2218 | 1 | chr2B.!!$F2 | 1021 |
11 | TraesCS3B01G030300 | chr1B | 567761980 | 567762519 | 539 | False | 334.000000 | 420 | 86.1305 | 481 | 953 | 2 | chr1B.!!$F2 | 472 |
12 | TraesCS3B01G030300 | chr7D | 21773849 | 21774970 | 1121 | False | 307.000000 | 307 | 72.5610 | 1122 | 2222 | 1 | chr7D.!!$F1 | 1100 |
13 | TraesCS3B01G030300 | chr2A | 11982108 | 11983249 | 1141 | True | 340.000000 | 340 | 73.0540 | 1106 | 2222 | 1 | chr2A.!!$R1 | 1116 |
14 | TraesCS3B01G030300 | chr7A | 22198099 | 22199220 | 1121 | False | 246.000000 | 246 | 71.6030 | 1122 | 2222 | 1 | chr7A.!!$F1 | 1100 |
AutoCloner calculated primer pairsThese primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible. |
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Position | MSA Position | Penalty | Sequence | TM | GC | Self any TH | Self end TH | Hairpin | End Stability | Orientation |
---|---|---|---|---|---|---|---|---|---|---|
635 | 636 | 0.106419 | AGTTTGGGCGGGAAAGACAA | 60.106 | 50.0 | 0.0 | 0.0 | 0.0 | 3.18 | F |
1539 | 1657 | 0.035439 | CCGTTTGCTCCCAGGTACAT | 60.035 | 55.0 | 0.0 | 0.0 | 0.0 | 2.29 | F |
Position | MSA Position | Penalty | Sequence | TM | GC | Self any TH | Self end TH | Hairpin | End Stability | Orientation |
---|---|---|---|---|---|---|---|---|---|---|
1831 | 1979 | 0.034756 | CACACCACCAACGATCCTGA | 59.965 | 55.0 | 0.0 | 0.0 | 0.00 | 3.86 | R |
2469 | 2650 | 0.097674 | GTCGATGTTGATGCAGTGGC | 59.902 | 55.0 | 0.0 | 0.0 | 41.68 | 5.01 | R |
All possible primersListed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives. |
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Based at the University of Bristol with support from BBSRC.
AutoCloner maintained by Alex Coulton.